Patenting your invention is about protecting your ideas and adding value to your company.  Part of that value lies in the reproducibility of your invention.  If you or anyone else are unable to reproduce your results, there is decreased value in your discovery and corresponding issues with scientific advancement, credibility, patentability and marketability.  The use of outdated tools and methods can contribute to difficulties with reproducibility and ultimately the value of your discovery and subsequent valuations of your company.
Part of receiving the limited monopoly of a patent is a contribution to the body of scientific knowledge.  In some ways, a patent can be viewed as a teaching document. In order for an invention to be enabled, as required for patentability, the specification must include enough information to allow someone of skill in the art to make and use the claimed invention.  In other words, your invention needs to be reproducible to be valid.
In a survey published in the journal Nature in January 2017, more than 70% of researchers revealed that they have tried and failed to reproduce another scientist’s results based on the information published in scientific literature (Munafò, Marcus R., Brian A. Nosek, Dorothy V. M. Bishop, Katherine S. Button, Christopher D. Chambers, Nathalie Percie Du Sert, Uri Simonsohn, Eric-Jan Wagenmakers, Jennifer J. Ware, and John P. A. Ioannidis. "A manifesto for reproducible science." Nature Human Behaviour1, no. 1 (2017): 0021. doi:10.1038/s41562-016-0021).  This reproducibility failure can call into question the validity of a patent that is based on research published in a paper.  If someone in the field cannot reproduce a claimed invention, then arguably the claimed invention is not enabled by the patent and therefore the claims are invalid.
As research becomes increasingly computerized, it is important to stay cognizant of software developments and updates as using outdated software may lead to conclusions that are not scientifically valid, and thus such conclusions may not be reproducible when updated software is utilized.  While it may be human nature to continue to rely on procedures and software you learned when you first started out, doing so may impact the patentability and any valuations attached to your discovery.
As an example, in the realm of computational biology, the website for TopHat, a spliced read mapper for RNA-Seq originally published in 2009, now states: “[p]lease note that TopHat has entered a low maintenance, low support stage as it is now largely superseded by HISAT2 which provides the same core functionality . . . in a more accurate and much more efficient way.” (Emphasis TopHat’s, https://ccb.jhu.edu/software/tophat/index.shtml).” TopHat has not been updated since February, 2016. 
In a letter to the editor published in Nature Methods in 2016 (Wadi, Lina, Mona Meyer, Joel Weiser, Lincoln D. Stein, and Jüri Reimand. "Impact of outdated gene annotations on pathway enrichment analysis." Nature Methods13, no. 9 (2016): 705-06. doi:10.1038/nmeth.3963), the authors wrote that “the use of outdated resources has strongly affected practical genomic analysis and recent literature: 67% of ∼3,900 publications we surveyed in 2015 referenced outdated software that captured only 26% of biological processes and pathways identified using current resources.”  What this means is that competitors using more advanced tools and methods have access to differentiating data and models that can be used, either in whole or part with existing knowledge, to more completely describe inventions. This may allow them to either to design around your claims or claim complete novelty.
Enablement is a requirement of patentability.  When “the claimed subject matter is inoperable, the patent may indeed be invalid for failure to meet the utility requirement of § 101 and the enablement requirement of § 112,” Process Control Corp. v. HydReclaim Corp. 190 F. 3d 1350 (Fed. Cir. 1999) citing Brooktree Corp., 977 F.2d at 1571, 24 USPQ2d at 1412 (citing Raytheon Co., 724 F.2d at 956, 220 USPQ at 596). Using the most modern tools and methods not only helps increase the breadth of your discovery, it also helps with reproducibility and validation of your claims.  Your insights and research are cutting edge, make sure your tools are, too.