- There is no chapter to date (that we know of) that has refused to fight simply because they were worried about the future of their geneseed.
- Chapters, units, and individuals have all surrendered and abandoned battles to save themselves or for their own purposes; but not from the stance of geneseed.
- It is more honorable to perish in battle than to retreat to be able to fight another day.
- The exception to this is in protecting the honor and memory of the chapter... then all bets are off and they will do anything they deem necessary...
- Honor > Survival
So your question surrounds the primary idea of a chapter abandoning a fight to preserve the future of their geneseed specifically. There is no example that we have to date of a chapter acting in such a manner, though it is possible.
Games Workshop and Black Library authors have all explored the mindset of the Space Marine and caused him to develop drastically over the years. In the beginning they were kind of just fearless monks that fought until death. Today, they have feelings, thoughts, etc. that drive actions both expected and otherwise.
There are units and individuals that have abandoned their tenants and sworn allegiance to Chaos (or simply become Rogue Marines) in order to save their own lives. This has changed the "Know no Fear" tenant for many to more that the indoctrination they have undergone doesn't remove all fear, but grants a heightened ability to conquer the fears they face.
And if a group is willing to lose their honor to save their lives it is entirely possible that an entire chapter could abandon a fight to ensure their chapter's survival.
That being said, as you mention, chapters consistently act according to their own desires. For example, the Dark Angels pursuing the Fallen. This can be seen as a form of preserving their chapter's future. The geneseed is not the goal here, but if knowledge of the chapter's secrets became public knowledge the chapter could be deemed as traitors, excommunicated, and destroyed. Worse however, would be that the lasting memory of the chapter would be tarnished. When spoken of in the future the chapter would not be referred to in reverence, but in disgust.
Many of the actions taken are done more to protect the lasting image of the chapter rather than preserve their survival. A chapter is much more concerned with maintaining their honor, respect, and status than surviving.
There have been an untold number of instances where a group goes into battle knowing full well they will not survive. More closely related to you question, they also will go back into battle or redouble efforts to retrieve a fallen geneseed or chapter treasure, willing to lose more to retrieve the priceless artifact.
I do not know if there is an official statement anywhere, but I have inferred over the years that chapters house a certain number of geneseed in their fortress-monasteries securely stashed in vaults. It is known that Chaos units will invade loyal chapters to steal the less corrupt seeds from their vaults to replace their own. It would make sense that a chapter would save a certain percentage of seed in an attempt to safeguard against the very situations you describe...
One final thought: There is also nothing that really says a chapter can't have a sort of hiatus from major conflicts to help rebuild their numbers when dangerously diminished. They could send word to the High Lords that they are in danger of being destroyed and obtain an a 'handicap' status requesting both engagements that carry less risk and another chapter's backup to protect their domain until they are back to fighting form. Such a request would also make sense. Another chapter sending some backup to aid a weakened chapter would be smarter than simply allowing a chapter to be destroyed and leave a domain unguarded...